data_CIV
# 
_chem_comp.id                                    CIV 
_chem_comp.name                                  "2-[2-[(1~{S})-1,5-bis(azanyl)pentyl]-4-[(4-hydroxyphenyl)methyl]-5-oxidanylidene-imidazol-1-yl]ethanamide" 
_chem_comp.type                                  "L-peptide linking" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C17 H23 N4 O4" 
_chem_comp.mon_nstd_parent_comp_id               "LYS, TYR, GLY" 
_chem_comp.pdbx_synonyms                         "CHROMOPHORE (LYS-TYR-GLY)" 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2021-11-22 
_chem_comp.pdbx_modified_date                    2024-09-27 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        347.389 
_chem_comp.one_letter_code                       KYG 
_chem_comp.three_letter_code                     CIV 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        7SWU 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              Y 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
CIV N1   N1   N 0 1 N N N Y Y N 5.767  10.876 39.079 1.151  0.934  -2.451 N1   CIV 1  
CIV CA1  CA1  C 0 1 N N S N Y N 6.006  12.272 39.546 1.626  0.505  -1.129 CA1  CIV 2  
CIV CB1  CB1  C 0 1 N N N N N N 4.708  13.081 39.574 1.449  1.648  -0.127 CB1  CIV 3  
CIV CG1  CG1  C 0 1 N N N N N N 4.199  13.295 38.146 2.353  2.818  -0.523 CG1  CIV 4  
CIV C1   C1   C 0 1 N N N N Y N 6.681  12.188 40.891 0.830  -0.690 -0.673 C1   CIV 5  
CIV N2   N2   N 0 1 N N N N Y N 6.120  12.526 42.033 -0.499 -0.657 -0.384 N2   CIV 6  
CIV N3   N3   N 1 1 N N N N Y N 7.967  11.764 41.093 1.330  -1.885 -0.511 N3   CIV 7  
CIV C2   C2   C 0 1 N N N N Y N 8.276  11.846 42.431 0.326  -2.716 -0.092 C2   CIV 8  
CIV O2   O2   O 0 1 N N N N Y N 9.385  11.515 42.915 0.404  -3.895 0.162  O2   CIV 9  
CIV CA2  CA2  C 0 1 N N N N Y N 7.076  12.325 43.021 -0.896 -1.842 -0.020 CA2  CIV 10 
CIV CA3  CA3  C 0 1 N N N N Y N 8.819  11.063 40.150 2.724  -2.270 -0.740 CA3  CIV 11 
CIV C3   C3   C 0 1 N N N N Y Y 9.690  11.939 39.266 3.356  -2.672 0.568  C3   CIV 12 
CIV O3   O3   O 0 1 N N N N Y Y 10.481 11.388 38.494 2.707  -2.639 1.587  O3   CIV 13 
CIV CB2  CB2  C 0 1 N N N N N N 6.714  12.607 44.448 -2.289 -2.252 0.387  CB2  CIV 14 
CIV CG2  CG2  C 0 1 Y N N N N N 7.481  11.812 45.481 -3.205 -1.058 0.313  CG2  CIV 15 
CIV CD1  CD1  C 0 1 Y N N N N N 7.873  12.399 46.676 -3.880 -0.778 -0.861 CD1  CIV 16 
CIV CD2  CD2  C 0 1 Y N N N N N 7.835  10.488 45.256 -3.375 -0.249 1.421  CD2  CIV 17 
CIV CE1  CE1  C 0 1 Y N N N N N 8.642  11.710 47.596 -4.721 0.316  -0.932 CE1  CIV 18 
CIV CE2  CE2  C 0 1 Y N N N N N 8.628  9.799  46.152 -4.216 0.846  1.356  CE2  CIV 19 
CIV CZ   CZ   C 0 1 Y N N N N N 9.058  10.421 47.316 -4.889 1.133  0.177  CZ   CIV 20 
CIV OH   OH   O 0 1 N N N N N N 9.821  9.762  48.228 -5.717 2.209  0.110  OH   CIV 21 
CIV CD   CD   C 0 1 N N N N N N 2.907  14.111 38.107 2.176  3.961  0.479  CD   CIV 22 
CIV CE   CE   C 0 1 N N N N N N 2.476  14.428 36.684 3.080  5.130  0.083  CE   CIV 23 
CIV NZ   NZ   N 0 1 N N N N N N 3.211  15.567 36.114 2.910  6.227  1.045  NZ   CIV 24 
CIV H    H1   H 0 1 N N N Y Y N 6.632  10.374 39.072 1.343  0.232  -3.150 H    CIV 25 
CIV H2   HN11 H 0 1 N Y N Y Y N 5.124  10.423 39.697 0.168  1.161  -2.426 H2   CIV 26 
CIV HA1  HA1  H 0 1 N N N N Y N 6.697  12.761 38.843 2.681  0.237  -1.191 HA1  CIV 27 
CIV HB11 HB11 H 0 0 N N N N N N 4.896  14.057 40.045 0.409  1.976  -0.131 HB11 CIV 28 
CIV HB12 HB12 H 0 0 N N N N N N 3.950  12.535 40.154 1.718  1.302  0.871  HB12 CIV 29 
CIV HG12 HG12 H 0 0 N N N N N N 4.011  12.313 37.686 3.393  2.490  -0.520 HG12 CIV 30 
CIV HG11 HG11 H 0 0 N N N N N N 4.971  13.827 37.571 2.084  3.164  -1.521 HG11 CIV 31 
CIV HA32 HA32 H 0 0 N N N N Y N 8.173  10.460 39.495 2.760  -3.110 -1.434 HA32 CIV 32 
CIV HA31 HA31 H 0 0 N N N N Y N 9.482  10.398 40.724 3.270  -1.427 -1.163 HA31 CIV 33 
CIV HB2  HB2  H 0 1 N N N N N N 6.894  13.675 44.639 -2.649 -3.029 -0.286 HB2  CIV 34 
CIV H5   H5   H 0 1 N N N N N N 5.644  12.387 44.576 -2.271 -2.634 1.408  H5   CIV 35 
CIV HD1  HD1  H 0 1 N N N N N N 7.572  13.413 46.892 -3.749 -1.414 -1.724 HD1  CIV 36 
CIV HD2  HD2  H 0 1 N N N N N N 7.484  9.989  44.365 -2.851 -0.472 2.338  HD2  CIV 37 
CIV HE1  HE1  H 0 1 N N N N N N 8.917  12.177 48.530 -5.247 0.535  -1.849 HE1  CIV 38 
CIV HE2  HE2  H 0 1 N N N N N N 8.913  8.778  45.947 -4.348 1.478  2.221  HE2  CIV 39 
CIV HOH  HOH  H 0 1 N N N N N N 10.018 10.342 48.954 -5.280 3.024  -0.172 HOH  CIV 40 
CIV HD2A HD2A H 0 0 N N N N N N 3.067  15.055 38.648 1.136  4.288  0.476  HD2A CIV 41 
CIV HD1A HD1A H 0 0 N N N N N N 2.109  13.536 38.600 2.445  3.614  1.477  HD1A CIV 42 
CIV HE2A HE2A H 0 0 N N N N N N 1.402  14.666 36.685 4.120  4.802  0.087  HE2A CIV 43 
CIV HE1A HE1A H 0 0 N N N N N N 2.655  13.543 36.056 2.812  5.476  -0.914 HE1A CIV 44 
CIV OXT  OXT  O 0 1 N Y N N Y Y 9.392  13.252 39.105 4.639  -3.066 0.602  O1   CIV 45 
CIV HXT  HXT  H 0 1 N Y N N Y Y 9.871  13.597 38.360 4.999  -3.313 1.464  H1   CIV 46 
CIV H3   H3   H 0 1 N N N N N N 2.893  15.736 35.181 3.091  5.914  1.987  H3   CIV 47 
CIV H4   H4   H 0 1 N N N N N N 3.051  16.380 36.673 3.497  7.012  0.806  H4   CIV 48 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
CIV NZ  CE   SING N N 1  
CIV CE  CD   SING N N 2  
CIV CD  CG1  SING N N 3  
CIV CG1 CB1  SING N N 4  
CIV O3  C3   DOUB N N 5  
CIV N1  CA1  SING N N 6  
CIV C3  CA3  SING N N 7  
CIV CA1 CB1  SING N N 8  
CIV CA1 C1   SING N N 9  
CIV CA3 N3   SING N N 10 
CIV C1  N3   DOUB N N 11 
CIV C1  N2   SING N N 12 
CIV N3  C2   SING N N 13 
CIV N2  CA2  DOUB N N 14 
CIV C2  O2   DOUB N N 15 
CIV C2  CA2  SING N N 16 
CIV CA2 CB2  SING N N 17 
CIV CB2 CG2  SING N N 18 
CIV CD2 CG2  DOUB Y N 19 
CIV CD2 CE2  SING Y N 20 
CIV CG2 CD1  SING Y N 21 
CIV CE2 CZ   DOUB Y N 22 
CIV CD1 CE1  DOUB Y N 23 
CIV CZ  CE1  SING Y N 24 
CIV CZ  OH   SING N N 25 
CIV N1  H    SING N N 26 
CIV N1  H2   SING N N 27 
CIV CA1 HA1  SING N N 28 
CIV CB1 HB11 SING N N 29 
CIV CB1 HB12 SING N N 30 
CIV CG1 HG12 SING N N 31 
CIV CG1 HG11 SING N N 32 
CIV CA3 HA32 SING N N 33 
CIV CA3 HA31 SING N N 34 
CIV CB2 HB2  SING N N 35 
CIV CB2 H5   SING N N 36 
CIV CD1 HD1  SING N N 37 
CIV CD2 HD2  SING N N 38 
CIV CE1 HE1  SING N N 39 
CIV CE2 HE2  SING N N 40 
CIV OH  HOH  SING N N 41 
CIV CD  HD2A SING N N 42 
CIV CD  HD1A SING N N 43 
CIV CE  HE2A SING N N 44 
CIV CE  HE1A SING N N 45 
CIV C3  OXT  SING N N 46 
CIV OXT HXT  SING N N 47 
CIV NZ  H3   SING N N 48 
CIV NZ  H4   SING N N 49 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
CIV SMILES           ACDLabs              12.01 "NCCCCC(N)C=1N=C(Cc2ccc(O)cc2)C(=O)[N+]=1CC(N)=O"                                                                                                     
CIV InChI            InChI                1.06  "InChI=1S/C17H22N4O4/c18-8-2-1-3-13(19)16-20-14(17(25)21(16)10-15(23)24)9-11-4-6-12(22)7-5-11/h4-7,13H,1-3,8-10,18-19H2,(H-,22,23,24)/p+1/t13-/m0/s1" 
CIV InChIKey         InChI                1.06  UNAYNKWNLZGKRW-ZDUSSCGKSA-O                                                                                                                           
CIV SMILES_CANONICAL CACTVS               3.385 "NCCCC[C@H](N)C1=[N+](CC(O)=O)C(=O)C(=N1)Cc2ccc(O)cc2"                                                                                                
CIV SMILES           CACTVS               3.385 "NCCCC[CH](N)C1=[N+](CC(O)=O)C(=O)C(=N1)Cc2ccc(O)cc2"                                                                                                 
CIV SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(ccc1CC2=NC(=[N+](C2=O)CC(=O)O)[C@H](CCCCN)N)O"                                                                                                  
CIV SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc(ccc1CC2=NC(=[N+](C2=O)CC(=O)O)C(CCCCN)N)O"                                                                                                      
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
CIV "SYSTEMATIC NAME" ACDLabs              12.01 "3-(2-amino-2-oxoethyl)-2-[(1S)-1,5-diaminopentyl]-5-[(4-hydroxyphenyl)methyl]-4-oxo-4H-imidazol-3-ium"              
CIV "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[2-[(1~{S})-1,5-bis(azanyl)pentyl]-4-[(4-hydroxyphenyl)methyl]-5-oxidanylidene-imidazol-1-ium-1-yl]ethanoic acid" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      CIV 
_pdbx_chem_comp_synonyms.name         "CHROMOPHORE (LYS-TYR-GLY)" 
_pdbx_chem_comp_synonyms.provenance   ? 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
CIV "Create component"   2021-11-22 RCSB 
CIV "Initial release"    2022-04-20 RCSB 
CIV "Modify backbone"    2023-11-03 PDBE 
CIV "Modify synonyms"    2024-05-06 PDBE 
CIV "Other modification" 2024-06-28 PDBE 
CIV "Modify PCM"         2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            CIV 
_pdbx_chem_comp_pcm.modified_residue_id                "LYS, TYR, GLY" 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           Chromophore/chromophore-like 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain and backbone" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               ? 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   ? 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
